The Royal Pirate
by iWant9Lives2Live
Summary: Emma is a princess who ran away on her eighteenth birthday, seeking passage on a pirate ship. What will happen between her and the future captain? Will her family ever find her? Will she have her happy ever after? Read to find out! Please review! (I am now adding more Captain Swan one shots but I need ideas- See 2nd chapter)
1. Chapter 1

_**This is my first ever Once Upon A Time fic so please give it a chance**_

_**The Royal Pirate**_

"Emma, dear, please get dressed quickly. The ball is starting soon. And make sure you look your best. You are meeting your future husband tonight," my mother said the night of my eighteenth birthday.

"Yes, Mother. I will be out soon." I knew what I had to do. I had to be free. I couldn't live here and marry someone I could never love. Instead of reaching for my ball gown, I opened my closet and took out the peasant dress I asked one of the servants for. I quickly slipped into it and threw on my mother's old cloak over it. After lacing up my boots and pulling my hood over my head, I jumped out of the window and used the ivy as a ladder to the ground below.

I dashed to the first place I could think of that would take me far away from here. The docks.

I took a second to let the salty air of the sea wash over me before running over to what I knew was a famous pirate ship. The Jolly Roger. The ship of Captain Liam Jones.

The crew seemed to be very busy so I crept along the edges until I found a door that lead to the storage space below deck. The water rocked the ship and caused me to stumble over the old crates. I felt strong arms wrap around me to keep me from falling. I looked up at my savior to see two beautiful blue eyes staring back at me. Right when I was about to thank this man, he pushed me up against a tall stack of crates with a dagger to my throat.

"Who are you and what are you doing on my brother's ship?" he hissed at me.

"My name is Emma," I said in a surprisingly strong voice. "Emma Swan. I'm here to seek passage out of this kingdom." He looked deeply in my eyes and he must have seen something that showed him how desperate I was because he removed the dagger from my throat and took a step back.

"You're running away, aren't you?" he asked me in an alluring accent.

"How do you know?" I asked him nervously, curious if he would recognize me as the princess.

"I ran away from home, too. My brother and I had the same look in our eyes. And I hate to break it to you, Love, but you're somewhat of an open book.

"Can you please provide me safe passage?" I begged. "I refuse to go home."

"We're going to have to ask my brother. He's the captain after all." He tugged me by the elbow to go above deck. He turned back to me and added, "My name's Killian by the way. Killian Jones."

"Liam!" Killian called out when we got on deck. "Liam, I need to speak with you!"

"I believe I saw him go down to the captain's quarters to rest, Sir," said a chubby man with a red knit hat.

"Thank you, Smee." Killian continued to pull me across the ship to a door which led to the captain's room. "Liam, we have a stowaway."

Liam turned around and eyed me curiously. "Who are you and what are you doing on my ship?"

"My name is Emma Swan. People are going to start looking for me soon. I need safe passage out of this kingdom."

"Killian, do you trust her?" he asked, looking down at his little brother.

"I just met her, but oddly enough, yes, I do trust her for some reason. When I look at her, she looks as scared and alone as we were when we ran away a few years ago."

"Very well then. If Killian trusts you, then so do I. I will grant you safe passage. But you will be swabbing the deck every other day as your payment to this ship. Think you can handle that?"

"Yes, Captain. That won't be a problem," I said with a grateful smile.

"The only bedroom with an extra bed is Killian's. So you'll have to sleep in there."

"No problem."

"Great, you can start working on deck tomorrow. Killian will show you the ropes."

I just smiled appreciatively at the two brothers.

_**Two Months Later...**_

I looked up from where I was swabbing the deck when I heard angry screams coming from the port side. Killian and Liam thankfully bought me new clothes that consisted of flowing blouses, leather vests, and leather pants so I could move around more freely in these situations. Killian has even been training me in sword fighting. I grabbed a sword from one of the crewmates and charged towards the intruders. They were pirates with a ship that was clearly falling apart. They're here to steal the Jolly Roger.

I took down three of their men and was impaling another when I caught Liam's eye from across the deck just in time to see him drop, blood staining his shirt over his chest. "Captain!" I screamed.

I charged towards the other ship's captain and sliced him across the stomach causing him to bleed out. I turned from him just in time to see Killian cradling his brother in his arms as he took his last breath. "Killian, I am so sorry. He was a great captain."

"Thank you, Swan," he said with tears in his eyes. "For taking care of his assailant."

"No problem. I'd do it again if I had the chance. Liam was always kind to me."

"What am I supposed to do now?"

"We need a new captain, Killian. It's time for you to lead the crew along with anyone who will like to join from the other crew."

"You're amazing, you know that?"

"I didn't actually. But maybe you can remind me later, Captain?"

"Absolutely." He smiled at me before standing up and making a moving speech that caused our crew and the others to cheer.

"Captain Jones! Captain Jones!" I chanted along with the crew.

_**One Month Later…**_

"Swan, are you alright?" Killian asked me as I entered the captain's quarters, his new bedroom.

"I had another nightmare. They always seem to go away after we have one of our chats. I'm still scared something is going to happen to you." Over the past month, my feelings for Killian have intensified. I can't stop thinking about him. But I know that nothing can happen. He's the captain. He doesn't want to be with a stowaway turned crewmate.

"Well, come in then. Let's talk." I sat next to him on his bed and ignored the sparks that went through me as his hand rested on my knee like he always did. "Why are you always so scared something will happen to me?"

"I'm scared because of what happened to Liam! I can't lose you!" I suddenly realized what that sounded like and rushed to correct myself. "I-I mean…the crew…the crew can't lose you. We-we all need you!"

"Emma, you want me to be safe for some reason other than the crew. What's this really about, Love?"

"Killian, I have feelings for you. Feelings I probably shouldn't have for the ship's captain." I was shaking, scared of what he was going to say. Would he laugh at me? Mock me? I was expecting anything except for what he actually did next.

He slowly leaned forward and gently pressed his lips to mine. His right hand wrapped around my waist while the other fisted in my hair to deepen the kiss. I wrapped my arms around his neck, trying to get him closer. He pulled away, leaving me breathless. He smiled at me and said, "I've had feelings for you since I met you, Love. I had told Liam and he told me not to act upon them. He said that it would make you nervous and you would question the intentions of a pirate."

"I would have never questioned you, Killian. You have been nothing but kind and considerate ever since I met you. Aside from the dagger to my throat, of course." He smiled and kissed me softly once again.

"Perhaps you should try going back to sleep, Love."

"Can I stay here? I don't want to be alone tonight." He motioned towards the bed and gestured for me to lay down. He laid down next to me and wrapped his arms around me from behind. That night, I fell asleep with an unstoppable smile on my face.

_**Six Months Later…**_

Things with Killian have been going amazingly well. Stolen kisses when the crew isn't looking, even though they knew that we are together. Romantic walks along the beach after obtaining a few magic beans. The plan is to go to Neverland and since the island has been rumored to be hard to get away from, we made sure we had more than one in case Neverland isn't what we expected.

We got aboard the ship to see Rumplestiltskin, the Dark One, on board. "Hello, dearies! I believe you have something I want."

"I don't believe we do," Killian stated strongly. Rumple looked at me as if I was harboring a secret, which I was. I still haven't told anyone who I really am, not even Killian.

"Well, I want a couple things actually. First, I want the magic bean in your hand. Second, I want the girl that's in the other." Killian stood in front of me protectively.

"You will have neither. Go away, Crocodile!" He held my hand tightly and his fist clamped harder around the magic beam. But I've gotten pretty good at noticing his sleight of hand. He had pocketed the bean without the Dark One seeing. His left fist was now empty.

"I guess I'll just make sure you don't have the girl then." Before I could even blink, Rumple was next to me and had reached a hand into my chest to retrieve my heart. I had never felt a pain as unbearable as this. "Love is weakness, Dearie!"

"No!" Killian screamed, his hand tightening around mine. Rumple tried to pull my heart from my chest but it wouldn't budge. He kept trying, but he couldn't take it.

At that moment, I had come to a conclusion. "Love isn't weakness, _dearie_. It's strength." Something within me blasted Rumple back as soon as I came to this realization.

"You have _magic_?" the Dark One hissed. "But you don't know how to use it, meaning I can do this without you stopping me." He took a crewmate's sword and sliced it cleanly across Killian's wrist, effectively severing his closed hand.

"Killian!" I screamed as Killian cried out in agony. I released his hand to grab the ship's rope hook. I rushed at the Dark One and buried the hook in his chest. I thought I had effectively hurt him when he suddenly laughed.

"It's going to take a lot more than that, Dearie." He giggled once more before vanishing in a puff of red smoke—along with Killian's hand—causing the hook to fall to the floor. I picked it up and walked back over to Killian.

"Why didn't you tell me you have magic?" he asked me.

"I didn't know," I said simply. "I know I'm the product of true love and I guess that means that I'm destined for greatness. I don't know, that's what a seer told my parents before I was born. They never mentioned anything about me having magic though. Enough about that now. We need to get you to a doctor before that gets infected."

He took the hook from me and I saw a plan beginning to form in his blue eyes.

A couple days later, his arm was mostly healed. He got a brace to put there where he clicked the hook into pace. "Do you still care for me even though I am no longer whole? Does it bother you that I have a hook for a hand now?"

"No, it doesn't bother me," I told him. "I love you. All of you."

"I love you, too, Swan."

I slipped my hand into his pocket and pulled out a magic bean. "Where to, Captain?" He grinned and took the bean from me.

He tossed it into the ocean to open up a portal for the Jolly Roger. "Neverland!" he shouted over the wind and sea before turning the wheel towards the portal.

_**Six Months Later…**_

Killian, the crew, and I had been in Neverland for six months. I have been with the crew for fifteen months and I had spent twelve of those with Killian. When I was living at the castle, I never thought I would have a happy ending like this. Killian and I were laying on the beach after another battle against Peter Pan and his Lost Boys.

"Emma, for the past year that we have been together, we have been through a lot. I never thought that it was possible to love someone as much as I love you." He stood up and helped me up as well. He reached into the pocket of his leather jacket and got down on one knee. My hand went up to my mouth in shock. "Emma Swan, my love, will you marry me?"

"What do you think?" I said before going down to his level and kissing him deeply. He slipped the golden diamond ring on my left ring finger and kissed me again. "You didn't steal this, did you?" I asked teasingly.

"No, my mom gave it to Liam before she passed away." I smiled softly and kissed him sweetly. We went back onto the Jolly and told the crew our big news. They all cheered and congratulated us. "You know, once we get married, the Jolly Roger will be half yours. We'll be co-captains."

"I didn't even think about that," I said honestly. "How about you take me down to the captain's quarters so we can celebrate while the crew gets drunk?" I whispered in his ear seductively. He grinned and picked me up, running to our room with me laughing in his arms.

_**Three Months Later…**_

A month after we got engaged, we all left Neverland. A month after that, I was feeling sick and had finally gone to a doctor while we were in port just to find out I was pregnant. I was nervous to tell Killian. We never talked about having children.

I have known for a month and we just got married yesterday. I still have to tell Killian that he's going to be a father and I have to do it tonight because I am just starting to show now that I am two months along. We have been spending most of our time in our room instead of leaving the crew alone on the ship. Now Killian and I were laying on our bed, completely exposed to one another.

"Killian," I started, looking into his deep blue eyes. "There's something I have to tell you. It's something that I've known for a month now but I haven't known how to tell you."

"What is it, Love? You know you can tell me anything."

"I know, it's just something we've never talked about before."

"Nothing you can say will ever make me love you any less, Swan."

"Killian," I started, shaking slightly. "How would you feel about being a father?"

"I can't think of anything that would make me happier. Swan, are you… are you with child?" I could see tears shining in his eyes. A ghost of a smile started forming on his face.

As soon as I nodded, he took me in his arms, laughing happily, planting kisses down my body until he reached my belly. "Hey there, Lad. This is your papa. I can't wait to meet you my little pirate," he whispered.

"Lad?" I ask teasingly. "What if it's a lass?"

"That would be just as lovely. But it's a lad. I can feel it."

"Mother's intuition tells me it's a girl."

"Well, if it _is_ a girl, I bet she will be just as beautiful as her mother," he said before crawling back up to my eye level and kissed me deeply.

The next day, we told the crew. They were all ecstatic, talking about how they couldn't wait until our child was old enough to swordfight.

_**Five Years Later…**_

Killian and I were both right. Seven months after I told him I was pregnant, I gave birth to twins; one boy and one girl. Liam David Jones and Mary Ruth Jones. They are now both four years old. Almost five.

Killian still doesn't know anything about my lineage. I don't consider myself a princess anymore. I'm a pirate.

Now I was putting Liam and Mary down for a nap. "Where is she?" I heard an unfamiliar voice bellow. I could hear the clang of swords above deck.

"Mama, what was that?" Liam asked, fear shining in his baby blue eyes.

"I don't know," I answer him. Mary curls into my lap, shaking. I set her next to Liam and grab my sword. "Liam, stay down here with Mary. I'm going to make sure your father is okay."

I ran up the stairs with my sword drawn. All of our crew members were tied up. Killian was cornered against the railing. Smee was the closest crew member tied next to me. He kicked a discarded sword closer to me. I picked it up in my free hand and approached the intruders slowly. "Where is my daughter?" the leader asked my husband. The man was clearly a king.

"I already told you. I don't kidnap princesses. We used to but my wife is against it so we stopped."

"What kind of foolish girl would marry _Captain Hook_?" The king said his moniker like it tasted foul in his mouth.

"Who are you calling foolish, your _majesty_?" I asked with the same tone. I rested the tips of the swords against the middle of the king's back. A smirk formed on Killian's handsome face. "Turn around slowly and have your men go back to your ship."

"Go," he told them. They slowly crossed the gap back to their own ship. The king turned around slowly and my breath caught in my throat.

My hat was covering half of my face with my head bowed down so he hasn't seen my face. But I saw a glimpse of his. "I know you have her on this ship. Several witnesses saw her on this ship about seven years ago."

"Did you ever think that maybe she went willingly? That maybe she wasn't kidnapped?"

"You don't know her. She never would have traded our life to live with filthy pirates like you."

Killian took my spare sword and pointed it at the king. "That's my wife you're talking to, _mate_."

"Um, Captain Swan, ma'am," I heard from not too far away. "Could we have some assistance?" Smee asked.

"A female captain?" the king asked incredulously.

"The title came with the marriage. I believe it is time you leave our ship." My head was still down so he couldn't see me.

"Not until you tell me where she is." I lowered my sword slightly.

"If I tell you where she is, will you leave my family and crew unharmed?"

"Of course. Why did you take her? For ransom?"

"We didn't take her," I argued. "She snuck onto the Jolly Roger willingly."

"I already told you; she wouldn't have done that."

"Perhaps you didn't know her as well as you thought you did."

"Swan…what are you saying?" Killian asked softly from my side.

I handed him my sword, my head still down. "I'm sorry, Killian. I was going to tell you. But then I fell in love with you. I figured you would never look at me the same way again." I carefully took off my hat and lifted my head, staring the king in the eye.

"Emma?" he whispered in a broken voice, his hand coming up to rest on my cheek.

"Hello, Father."

"Why did you run away? We have been looking for you since your eighteenth birthday. That is six and a half years not knowing where our daughter was."

"I'm sorry, Father, but did you not hear me? I'm married to a man I love with all my soul, who I hope will still have me?" I asked as I slowly turned to face my husband.

"Do you remember what you told me the night after our wedding? You didn't know how to tell me and I said…" he trailed off, hoping for me to finish it.

"You said that there was nothing I could tell you that would make you love me any less," I said with a small smile.

"And I meant it, Love." I smiled and kissed him lightly.

"As touching as this is, you have to come home, Emma."

"I'm not going to leave Killian!"

"Mama?" I heard from a few feet away.

"Mary? Liam David Jones!" I yelled out, knowing that he would never be too far away from his sister. He's very protective of her. He poked his head out from the office next to Mary. I briefly saw my father grin when he heard my son's middle name.

"Yes, Mama?" he asked shyly. I motioned for both of them to come closer. Once they were in arm's length, I grabbed each of their hands.

"I told you to keep your sister below deck."

"Sorry, Mama. But Mary's fast." I couldn't help the fond smile that stretched across my face.

I stood back up to my father's height. "I can't leave this life behind. They're my family. If I had stayed that night, I would have married someone I didn't love. With Killian, it was love at first sight. I just didn't realize until a couple months later. I was hoping that if you or Mother ever caught me, you would understand. You both found true love. And now so have I."

"Come home." Out of the corner of my eye, I could see Killian finally untying the crew. "Why did your crew become pirates?"

"They were poor. Most of them lost their family to the plague. The others were born without a family. They needed money so they joined this lifestyle. Killian and his brother, Liam, were in the navy in a kingdom with a ruthless king who wanted to win war unfairly. Their ship separated from the navy so they wouldn't be controlled anymore. Before the navy, they were children in the streets who ran away from an unloving family after their mother died. They wanted freedom, which is why I left. I wanted to be free."

"Emma, do you consider me to be a fair king?"

"Yes, of course, Father."

"If you come home, I can arrange the crew to join our navy. All of them will be well off and they can start their own families. We can even provide them shelter. You and your family will live in the palace, of course."

I turned to my gorgeous husband. "Would you like that? You'd be a prince."

"I can handle it, Love. As long as you are by my side," he said in that amazing accent I fell in love with. He rested his forehead against mine before crashing his lips on top of mine.

_**One Month Later…**_

The kingdom welcomed Killian and I with open arms. My mother, who Killian insisted on calling Lady Snow, was very ecstatic. She was even happier when she met her grandchildren.

I was now standing in the doorway of the guest room next door to mine and Killian's bedroom. Strong arms wrapped around my waist. "What are you doing in here, Love?"

I leaned my head back against his chest, one of my hands resting on his right arm while the other lightly caressed his hook. "I was just thinking; is this room big enough for a nursery?"

"Swan… are… are you pregnant?" I nodded happily. He spun me around to face him, kissed me deeply, picked me up, and spun me around.

"What's going on here?" Mother asked with Father by her side.

"We are having another child," I told them excitedly. They both hugged me and my husband.

Eight months later, I gave birth to a beautiful baby boy. Prince Henry Neal Jones.

And they all lived happily ever after…

_**Well, there you go. Remember, this is my first Once Upon a Time story so please don't be too harsh. Sorry if it seems really rushed. Sorry if there are a lot of mistakes. I wrote this on my phone. And sometimes my phone randomly deletes words. I don't know how. I tried my best. Please review! ! !**_


	2. Prompts?

I am going to be adding to this with more Captain Swan one shots. But I need ideas for these one shots so please help me by sending me prompts through PM or go to the new forum I posted called "Captain Swan Prompts?".

Thank you. If you have any questions, PM me please.


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